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SAFB2 Gene

protein-coding   GIFtS: 59

GC19M005538
scaffold attachment factor B2
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
KIAA0138 1, 2, 3, 5
SAF-B2 3
Descriptions
scaffold attachment factor B2 2
External Ids
HGNC: 216051
Entrez Gene: 96672
UniProtKB: Q141513
Ensembl: ENSG000001302547
Search outside databases for aliases for SAFB2 gene

Previous GC identifer: GC19M005527

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: SAFB2_HUMAN, Q14151
Function: Binds to scaffold/matrix attachment region (S/MAR) DNA. Can function as an estrogen
receptor corepressor and can also inhibit cell proliferation

Gene Wiki entry for SAFB2

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the SAFB2 gene  

Entrez Gene cytogenetic band: 19p13.3   Ensembl cytogenetic band:  19p13.3   HGNC cytogenetic band: 19p13.3

SAFB2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M005538:     (about GC identifiers)

Start:
5,538,010 bp from pter
End:
5,573,938 bp from pter
Size:
35,929 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000019.8  NT_011255.14  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: SAFB2_HUMAN, Q14151 (See protein sequence)
Recommended Name: Scaffold attachment factor B2  
Size: 953 amino acids; 107473 Da
Subunit: Interacts with SAFB/SAFB1 and SCAM1
Subcellular location: Cytoplasm. Nucleus
Secondary accessions: Q8TB13

Post-translational modifications:

  • Phosphorylated upon DNA damage, probably by ATM or ATR (By similarity)1
  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_055464.1  

    ENSEMBL proteins: 
    ENSP00000378122 ENSP00000252542 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (Scaffold attachment factor B2)
    Human Recombinant Proteins from Abnova (SAFB2)
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    2 Gene Ontology (GO) cellular component terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634 nucleus IEA--
    GO:0005737 cytoplasm IEA--
    About this table

    Antibodies for SAFB2: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for SAFB2
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (Scaffold attachment factor B2), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (SAFB2)
    Novus Biologicals Antibodies for SAFB2

    Assays for SAFB2: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    3 InterPro domains/families:
     IPR003034 SAP_DNA_bd
     IPR000504 RRM_RNP1
     IPR012677 a_b_plait_nuc_bd


       GeneDecks  SAFB2 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q14151

    ProtoNet protein and cluster: Q14151

    2 Blocks protein families:
    IPB000504 RNA-binding region RNP-1 (RNA recognition motif)
    IPB003034 DNA-binding SAP


    UniProtKB/Swiss-Prot: SAFB2_HUMAN, Q14151
    Similarity: Contains 1 RRM (RNA recognition motif) domain
    Similarity: Contains 1 SAP domain

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (SAFB2)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (SAFB2)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_014649

                  Applied Biosystems Silencer® siRNAs for SAFB2

                  Sigma-Aldrich siRNA for SAFB2  
                         Sigma-Aldrich shRNA for SAFB2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for SAFB2
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_014649
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_014649
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_014649 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_014649

    UniProtKB/Swiss-Prot: SAFB2_HUMAN, Q14151
    Function: Binds to scaffold/matrix attachment region (S/MAR) DNA. Can function as an estrogen
    receptor corepressor and can also inhibit cell proliferation

    3 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166 nucleotide binding IEA--
    GO:0003677 DNA binding IEA--
    GO:0003723 RNA binding IEA--
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section



    4 Interacting proteins for SAFB2 (ENSP000002525423 Q141512) via UniProtKB, MINT, and/or STRING
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CHGBP050602MINT-64171
    SORBS3ENSP000002401233STRING (score=.957)
    ESR1ENSP000002062493STRING (score=.946)
    --ENSP000003610633STRING (score=.722)
    About this table

    2 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006350 transcription IEA--
    GO:0006355 regulation of transcription, DNA-dependent IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for SAFB2

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (SAFB2)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (SAFB2)
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_014649

                  Sigma-Aldrich siRNA for SAFB2  
                         Sigma-Aldrich shRNA for SAFB2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_014649  

    REFSEQ mRNAs for SAFB2 gene: 

    NM_014649.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_014649  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_014649
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_014649
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_014649 

    Additional cDNA sequence: 

    AK123246.1 AK296552.1 AK300501.1 BC001216.1 BC014784.1 BC025279.1 D50928.1 

    24/26 DOTS entries (see all 26 ):

    DT.95284311  DT.75176560  DT.99958547  DT.99977968  DT.40110022  DT.100814583  DT.121455574  DT.97860337 
    DT.100737017  DT.40280613  DT.75103418  DT.91742864  DT.40306882  DT.75119206  DT.92030453  DT.121455580 
    DT.450237  DT.91863535  DT.95363107  DT.100040325  DT.100811853  DT.65287715  DT.97819785  DT.97820339 

    24/194 AceView cDNA sequences (see all 194 ):

    BC014784 BM764466 AI168419 BU181609 CK430953 BQ672926 BE395325 BM708690 
    BM174910 BM683580 BQ920969 BE252761 AK123246 BC001216 BU161744 BM929597 
    BU195637 BE018969 BQ058036 BM718536 BM765758 BX283817 BQ883292 BM746190 

    highest scoring ESTs for SAFB2:

    D50928 AI587127 BE830657 BG436879 BM559198 BM753564 BM765758 AA286987 AW383803 BF328019 

    Unigene Cluster for SAFB2:

    Scaffold attachment factor B2
    Hs.655392  [show with all ESTs]
    Unigene Representative Sequence: NM_014649


    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for SAFB2 (see all 8 )

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18a · 18b · 18c ^ 19 ^ 20a ·
    SP1:                                                                                                                                                            
    SP2:        -     -                                                                                                                                             
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 20b ^ 21
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            

    About this scheme

    ECgene alternative splicing isoforms for SAFB2

    2 Ensembl transcripts including schematic representations:
    ENST00000394625  ENST00000252542  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    SAFB2 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for SAFB2

    1 / 2 / 3

    5 probe-sets matching SAFB2 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    32099_at2, 3 U133-A 1 1.00 1.00 1.00 1.00 D50928 0.80 0.80 0.80 1

    32099_at2, 3 U133-A 1 1.00 1.00 -- -- D50928 0.80 0.80 0.80 1

    203280_at2, 3 U133-A 1 1.00 1.00 -- -- NM_014649 0.40 0.67 0.55 1

    32099_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    203280_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: TTGTAGCTCA

    SOURCE GeneReport for Unigene cluster: Hs.655392

    Expression variation in blood from EXPOLDB for SAFB2

    UniProtKB/Swiss-Prot: SAFB2_HUMAN, Q14151
    Tissue specificity: Expressed at high levels in the CNS and at low levels in the liver. Expressed
    in a wide number of breast cancer cell lines

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for SAFB2 gene from 5/8 species (see all 8 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    SAFB21   -- scaffold attachment factor B2 88.31(n)
    89.08(a)
    476740  XM_533945.2  XP_533945.2 
    chimpanzee
    (Pan troglodytes)
    SAFB21   -- scaffold attachment factor B2 99.58(n)
    99.69(a)
    455618  XM_512297.2  XP_512297.2 
    cow
    (Bos taurus)
    SAFB21   -- scaffold attachment factor B2 84.62(n)
    83.63(a)
    509045  XM_585928.3  XP_585928.3 
    mouse
    (Mus musculus)
    Safb21, 5 175
    scaffold attachment factor B21, 5 76.93(n)1
    74.26(a)1
    2249021  NM_001029979.11  NP_001025150.11 
     AA3894335  AI2551705  (see all 23)
    chicken
    (Gallus gallus)
    SAFB21   -- scaffold attachment factor B2 71.35(n)
    67.97(a)
    427046  XM_424644.2  XP_424644.2 
    About this table        Species with no ortholog for SAFB2

    ENSEMBL Gene Tree for SAFB2
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for SAFB2 gene
    SLTM2  SAFB2  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/143 NCBI SNPs in SAFB2 are shown (see all 143 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 54)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 19 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs48077911,2
    A,C,F5538144(+) CAACAT/CGGTGG 1 -- ut31 ese33Minor allele frequency- C:0.01NA 128
    rs20745921,2
    C,F,H5538177(+) AAGATC/ACCCCA 1 -- ut312Minor allele frequency- A:0.07EA EU 1616
    rs104129191,2
    A,C5537749(+) GGCCCC/TATGGT 1 -- ng510--------
    rs7334491,2
    F,H5537820(+) TCCCAT/CGATGG 1 -- ng5112Minor allele frequency- C:0.10NA EA EU WA 898
    rs8067061,2
    C,F,H,O5561045(-) ACACGC/TGCTAC 1 R/R syn15Minor allele frequency- T:0.03MN EU EA WA 598
    rs7399431,2
    A,C,F,H,O5550837(-) TTGTCC/TGAGTT 1 -- int18Minor allele frequency- T:0.40MN EU EA WA 2278
    rs8067101,2
    A,C,F,H,O5569444(+) CCACTG/ATTATC 1 -- int18Minor allele frequency- A:0.21EU EA WA 836
    rs8067041,2
    A,C,F,H,O5557259(+) tgtgtA/Cccaga 1 -- int18Minor allele frequency- C:0.25MN EU EA WA NA 734
    rs48077921,2
    A,C,F,H5538541(+) TCATCG/ACACAT 1 -- int17Minor allele frequency- A:0.01EU EA WA NA 560
    rs8067051,2
    A,C,F,H5558688(+) CACCAT/CTGGCG 1 -- int14Minor allele frequency- C:0.03EU EA WA 420
    About this table

    HapMap Linkage Disequilibrium images for SAFB2 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 608066

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/18 PubMed articles for SAFB2 gene (see all 18 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 9667 HGNC: 21605 AceView: SAFB2 Ensembl:ENSG00000130254 euGenes: HUgn9667
    ECgene: SAFB2 H-InvDB: SAFB2
    (According to HUGE)
    About This Section

    HUGE: KIAA0138
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

      --
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for SAFB2:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for SAFB2 Antibodies for SAFB2
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for SAFB2 Browse small molecules at Sigma-Aldrich
     "Your Favorite Gene" Pathwaysfeedback


      
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     Antibodies for SAFB2

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